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Basic properties for biological databases: Character development and support. (English) Zbl 0895.92004

Summary: We examine problems and solutions for building a large set of characters for descriptive data derived from published species descriptions. The ideas presented lead in the direction of creating a kind of BioDBMS that can be used to support large integrated biological databases.

MSC:

92B10 Taxonomy, cladistics, statistics in mathematical biology
68U99 Computing methodologies and applications
68P99 Theory of data
92-08 Computational methods for problems pertaining to biology
92B99 Mathematical biology in general
Full Text: DOI

References:

[1] Pankhurst, R. J., Database design for monographs and floras, Taxon, 37, 733-746 (1988)
[2] Allkin, R.; White, R. J.; Winfield, P. J., Handling the taxonomic structure of biological data, Mathl. Comput. Modelling, 16, 6/7, 1-9 (1992) · Zbl 0754.92003
[3] Dallwitz, M. J., DELTA and INTKEY, (Fortuner, R., Advances in Computer Methods for Systematic Biology (1993), Johns Hopkins University Press: Johns Hopkins University Press Baltimore), Chapter 18 · Zbl 0850.92002
[4] Dallwitz, M. J.; Paine, T. A., User’s guide to the DELTA system: A general system for processing taxonomic descriptions, CSIRO Aust. Div. Entomol. Rep. No. 13, 1-106 (1986), \(3^{rd}\) edition
[5] (Allkin, R.; Bisby, F. A., Databases in Systematics, Systematics Association, Vol. 26 (1984), Academic Press: Academic Press London)
[6] White, R. J.; Allkin, R.; Winfield, J. P., Systematic databases: The BAOBAB design and the Alice system, (Fortuner, R., Advances in Computer Methods for Systematic Biology (1993), Johns Hopkins University Press: Johns Hopkins University Press Baltimore), Chapter 19
[7] Pankhurst, R. J., Taxonomic databases: The Pandora system, (Fortuner, R., Advances in Computer Methods for Systematic Biology (1993), Johns Hopkins University Press: Johns Hopkins University Press Baltimore), Chapter 14 · Zbl 0519.92003
[8] White, R. J.; Allkin, R., A language for the definition and exchange of biological data sets, Mathl. Comput. Modelling, 16, 6/7, 199-223 (1992)
[9] Saarenmaa, H.; Leppäjärvi, S.; Perttunen, J.; Saarikko, J., (Object-oriented taxonomic biodiversity databases on the World Wide Web, from an international workshop: Internet Applications and Electronic Information Resources in Forestry and Environmental Sciences (1-5 August 1995), European Forest Institute: European Forest Institute Joensuu, Finland), and available through the web at
[10] Diederich, J.; Milton, J., Expert workstations: A tool-based approach, (Fortuner, R., Advances in Computer Methods for Systematic Biology (1993), Johns Hopkins University Press: Johns Hopkins University Press Baltimore), Chapter 7
[11] Diederich, J.; Milton, J., NEMISYS: A computer perspective, (Fortuner, R., Advances in Computer Methods for Systematic Biology (1993), Johns Hopkins University Press: Johns Hopkins University Press Baltimore), Chapter 10
[12] Fortuner, R., The NEMISYS solution to problems in nematode identification, (Fortuner, R., Advances in Computer Methods for Systematic Biology (1993), Johns Hopkins University Press: Johns Hopkins University Press Baltimore), Chapter 9 · Zbl 0850.92002
[13] J. Diederich, J. Milton and R. Fortuner, Construction and integration of large character sets for nematode morpho-anatomical data, Fundamental and Applied Nematology20 (to appear).; J. Diederich, J. Milton and R. Fortuner, Construction and integration of large character sets for nematode morpho-anatomical data, Fundamental and Applied Nematology20 (to appear).
[14] Allkin, R.; Bisby, F. A., The structure of monographic databases, Taxon, 37, 756-763 (1988)
[15] Wiederhold, G., Views, objects, and databases, Computer, 19, 12, 37-44 (Dec. 1986)
[16] Allkin, R.; Moreno, N. P.; Campillo, L. Gamà; Mejia, T., Multiple uses for computer-stored taxonomic descriptions: Keys for Veracruz, Taxon, 41, 3, 413-435 (1992)
[17] Chen, P., The entity-relationship model: Toward a unified view of data, ACM TODS, 1, 1, 9-36 (Mar. 1976)
[18] Hammer, M.; McLeod, D., Data description with SDM: A semantic data model, ACM TODS, 6, 3, 351-386 (Sept. 1981)
[19] Diederich, J.; Milton, J., Creating domain specific metadata for scientific data and knowledge bases, IEEE Trans, on Know and Data Eng., 3, 4, 421-434 (Dec. 1991)
[20] Special Issue on Scientific Databases. Special Issue on Scientific Databases, Bulletin of the technical committee on data engineering, IEEE Computer Society, Volume 16, No. 1 (1993), Washington, DC
[21] Shoshani, A., A layered approach to scientific data management projects at Lawrence Berkeley laboratory, (Data Engineering. Data Engineering, IEEE Computer Society, Volume 16 (1993)), 4-8, Washington, DC
[22] Ioannidis, Y., Desktop experiment management, (Data Engineering. Data Engineering, IEEE Computer Society, Vol. 16 (1993)), 19-23, Washington, DC
[23] Cushing, J. B.; Hansen, D.; Maier, D.; Pu, C., Connecting scientific programs and data using object databases, (Data Engineering. Data Engineering, IEEE Computer Society, Volume 16 (1993)), 9-13, Washington, DC
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